Can't execute `conda activate` from bash script

mjspeck commented 5 years ago

Current Behavior

Trying to use conda activate my_env does not work inside a bash script. The workaround is to use source activate my_env but this shouldn't be necessary.

Steps to Reproduce

Write a bash script with the following code inside, let's call it my-script.sh:

conda activate my_env

When you run ./my-script.sh, you get the following output:

CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'.
If your shell is Bash or a Bourne variant, enable conda for the current user with

    $ echo ". /Users/matthewspeck/anaconda3/etc/profile.d/conda.sh" >> ~/.bash_profile

or, for all users, enable conda with

    $ sudo ln -s /Users/matthewspeck/anaconda3/etc/profile.d/conda.sh /etc/profile.d/conda.sh

The options above will permanently enable the 'conda' command, but they do NOT
put conda's base (root) environment on PATH.  To do so, run

    $ conda activate

in your terminal, or to put the base environment on PATH permanently, run

    $ echo "conda activate" >> ~/.bash_profile

Previous to conda 4.4, the recommended way to activate conda was to modify PATH in
your ~/.bash_profile file.  You should manually remove the line that looks like

    export PATH="/Users/matthewspeck/anaconda3/bin:$PATH"

^^^ The above line should NO LONGER be in your ~/.bash_profile file! ^^^

However, conda is in fact installed correctly, and runs fine in the command line.

The command which conda returns the following:

conda () {
    if [ "$#" -lt 1 ]
    then
        $_CONDA_EXE
    else
        \local cmd="$1"
        shift
        case "$cmd" in
            (activate) _conda_activate "$@" ;;
            (deactivate) _conda_deactivate "$@" ;;
            (install | update | uninstall | remove) $_CONDA_EXE "$cmd" "$@" && _conda_reactivate ;;
            (*) $_CONDA_EXE "$cmd" "$@" ;;
        esac
    fi
}

Expected Behavior

conda should activate in a bash script the same way it does on the command line.

Environment Information

`conda info`

``` active environment : base active env location : /Users/matthewspeck/anaconda3 shell level : 1 user config file : /Users/matthewspeck/.condarc populated config files : /Users/matthewspeck/.condarc conda version : 4.5.11 conda-build version : 3.16.2 python version : 3.6.6.final.0 base environment : /Users/matthewspeck/anaconda3 (writable) channel URLs : https://repo.anaconda.com/pkgs/main/osx-64 https://repo.anaconda.com/pkgs/main/noarch https://repo.anaconda.com/pkgs/free/osx-64 https://repo.anaconda.com/pkgs/free/noarch https://repo.anaconda.com/pkgs/r/osx-64 https://repo.anaconda.com/pkgs/r/noarch https://repo.anaconda.com/pkgs/pro/osx-64 https://repo.anaconda.com/pkgs/pro/noarch package cache : /Users/matthewspeck/anaconda3/pkgs /Users/matthewspeck/.conda/pkgs envs directories : /Users/matthewspeck/anaconda3/envs /Users/matthewspeck/.conda/envs platform : osx-64 user-agent : conda/4.5.11 requests/2.20.0 CPython/3.6.6 Darwin/17.7.0 OSX/10.13.6 UID:GID : 501:20 netrc file : None offline mode : False ```

`conda config --show-sources`

``` ==> /Users/matthewspeck/.condarc <== ssl_verify: True channels: - defaults ```

`conda list --show-channel-urls`

``` # packages in environment at /Users/matthewspeck/anaconda3: # # Name Version Build Channel _ipyw_jlab_nb_ext_conf 0.1.0 py36_0 defaults alabaster 0.7.12 py36_0 defaults anaconda-client 1.7.2 py36_0 defaults anaconda-navigator 1.9.2 py36_0 defaults anaconda-project 0.8.2 py36_0 defaults appdirs 1.4.3 py36h28b3542_0 defaults appnope 0.1.0 py36hf537a9a_0 defaults appscript 1.0.1 py36h1de35cc_1 defaults asn1crypto 0.24.0 py36_0 defaults astroid 2.0.4 py36_0 defaults astropy 3.0.5 py36h1de35cc_0 defaults atomicwrites 1.2.1 py36_0 defaults attrs 18.2.0 py36h28b3542_0 defaults automat 0.7.0 py36_0 defaults babel 2.6.0 py36_0 defaults backcall 0.1.0 py36_0 defaults backports 1.0 py36_1 defaults backports.os 0.1.1 py36_0 defaults backports.shutil_get_terminal_size 1.0.0 py36_2 defaults beautifulsoup4 4.6.3 py36_0 defaults bitarray 0.8.3 py36h1de35cc_0 defaults bkcharts 0.2 py36h073222e_0 defaults blas 1.0 mkl defaults blaze 0.11.3 py36_0 defaults bleach 3.0.2 py36_0 defaults blosc 1.14.4 hd9629dc_0 defaults bokeh 1.0.1 py36_0 defaults boto 2.49.0 py36_0 defaults bottleneck 1.2.1 py36h1d22016_1 defaults bzip2 1.0.6 h1de35cc_5 defaults ca-certificates 2018.03.07 0 defaults certifi 2018.10.15 py36_0 defaults cffi 1.11.5 py36h6174b99_1 defaults chardet 3.0.4 py36_1 defaults click 7.0 py36_0 defaults cloudpickle 0.6.1 py36_0 defaults clyent 1.2.2 py36_1 defaults colorama 0.4.0 py36_0 defaults conda 4.5.11 py36_0 defaults conda-build 3.16.2 py36_0 defaults conda-env 2.6.0 1 defaults constantly 15.1.0 py36h28b3542_0 defaults contextlib2 0.5.5 py36hd66e5e7_0 defaults coverage 4.5.1 py36h1de35cc_0 defaults cryptography 2.3.1 py36hdbc3d79_0 defaults curl 7.61.0 ha441bb4_0 defaults cycler 0.10.0 py36hfc81398_0 defaults cython 0.29 py36h0a44026_0 defaults cytoolz 0.9.0.1 py36h1de35cc_1 defaults dask 0.20.0 py36_0 defaults dask-core 0.20.0 py36_0 defaults datashape 0.5.4 py36_1 defaults dbus 1.13.2 h760590f_1 defaults decorator 4.3.0 py36_0 defaults defusedxml 0.5.0 py36_1 defaults distributed 1.24.0 py36_0 defaults docutils 0.14 py36hbfde631_0 defaults entrypoints 0.2.3 py36_2 defaults et_xmlfile 1.0.1 py36h1315bdc_0 defaults expat 2.2.6 h0a44026_0 defaults fastcache 1.0.2 py36h1de35cc_2 defaults filelock 3.0.10 py36_0 defaults flask 1.0.2 py36_1 defaults flask-cors 3.0.6 py36_0 defaults freetype 2.9.1 hb4e5f40_0 defaults get_terminal_size 1.0.0 h7520d66_0 defaults gettext 0.19.8.1 h15daf44_3 defaults gevent 1.3.7 py36h1de35cc_1 defaults glib 2.56.2 hd9629dc_0 defaults glob2 0.6 py36_1 defaults gmp 6.1.2 hb37e062_1 defaults gmpy2 2.0.8 py36h6ef4df4_2 defaults greenlet 0.4.15 py36h1de35cc_0 defaults h5py 2.8.0 py36h878fce3_3 defaults hdf5 1.10.2 hfa1e0ec_1 defaults heapdict 1.0.0 py36_2 defaults html5lib 1.0.1 py36_0 defaults hyperlink 18.0.0 py36_0 defaults icu 58.2 h4b95b61_1 defaults idna 2.7 py36_0 defaults imageio 2.4.1 py36_0 defaults imagesize 1.1.0 py36_0 defaults importlib_metadata 0.6 py36_0 defaults incremental 17.5.0 py36_0 defaults intel-openmp 2019.0 118 defaults ipykernel 5.1.0 py36h39e3cac_0 defaults ipython 7.1.1 py36h39e3cac_0 defaults ipython_genutils 0.2.0 py36h241746c_0 defaults ipywidgets 7.4.2 py36_0 defaults isort 4.3.4 py36_0 defaults itsdangerous 1.1.0 py36_0 defaults jbig 2.1 h4d881f8_0 defaults jdcal 1.4 py36_0 defaults jedi 0.13.1 py36_0 defaults jinja2 2.10 py36_0 defaults jpeg 9b he5867d9_2 defaults jsonschema 2.6.0 py36hb385e00_0 defaults jupyter 1.0.0 py36_7 defaults jupyter_client 5.2.3 py36_0 defaults jupyter_console 6.0.0 py36_0 defaults jupyter_core 4.4.0 py36_0 defaults jupyterlab 0.35.3 py36_0 defaults jupyterlab_launcher 0.13.1 py36_0 defaults jupyterlab_server 0.2.0 py36_0 defaults keyring 16.0.0 py36_0 defaults kiwisolver 1.0.1 py36h0a44026_0 defaults lazy-object-proxy 1.3.1 py36h1de35cc_2 defaults libarchive 3.3.3 hc2e69e3_1 defaults libcurl 7.61.0 hf30b1f0_0 defaults libcxx 4.0.1 h579ed51_0 defaults libcxxabi 4.0.1 hebd6815_0 defaults libedit 3.1.20170329 hb402a30_2 defaults libffi 3.2.1 h475c297_4 defaults libgfortran 3.0.1 h93005f0_2 defaults libiconv 1.15 hdd342a3_7 defaults libpng 1.6.34 he12f830_0 defaults libsodium 1.0.16 h3efe00b_0 defaults libssh2 1.8.0 h322a93b_4 defaults libtiff 4.0.9 hcb84e12_2 defaults libxml2 2.9.8 hab757c2_1 defaults libxslt 1.1.32 hb819dd2_0 defaults llvmlite 0.25.0 py36h8c7ce04_0 defaults locket 0.2.0 py36hca03003_1 defaults lxml 4.2.5 py36hef8c89e_0 defaults lz4-c 1.8.1.2 h1de35cc_0 defaults lzo 2.10 h362108e_2 defaults markupsafe 1.0 py36h1de35cc_1 defaults matplotlib 3.0.0 py36h54f8f79_0 defaults mccabe 0.6.1 py36_1 defaults mistune 0.8.4 py36h1de35cc_0 defaults mkl 2019.0 118 defaults mkl-service 1.1.2 py36h6b9c3cc_5 defaults mkl_fft 1.0.6 py36hb8a8100_0 defaults mkl_random 1.0.1 py36h5d10147_1 defaults more-itertools 4.3.0 py36_0 defaults mpc 1.1.0 h6ef4df4_1 defaults mpfr 4.0.1 h3018a27_3 defaults mpmath 1.0.0 py36_2 defaults msgpack-python 0.5.6 py36h04f5b5a_1 defaults multipledispatch 0.6.0 py36_0 defaults navigator-updater 0.2.1 py36_0 defaults nbconvert 5.4.0 py36_1 defaults nbformat 4.4.0 py36h827af21_0 defaults ncurses 6.1 h0a44026_0 defaults networkx 2.2 py36_1 defaults nltk 3.3.0 py36_0 defaults nose 1.3.7 py36_2 defaults notebook 5.7.0 py36_0 defaults numba 0.40.0 py36h6440ff4_0 defaults numexpr 2.6.8 py36h1dc9127_0 defaults numpy 1.15.4 py36h6a91979_0 defaults numpy-base 1.15.4 py36h8a80b8c_0 defaults numpydoc 0.8.0 py36_0 defaults odo 0.5.1 py36hc1af34a_0 defaults olefile 0.46 py36_0 defaults openpyxl 2.5.9 py36_0 defaults openssl 1.0.2p h1de35cc_0 defaults packaging 18.0 py36_0 defaults pandas 0.23.4 py36h6440ff4_0 defaults pandoc 1.19.2.1 ha5e8f32_1 defaults pandocfilters 1.4.2 py36_1 defaults parso 0.3.1 py36_0 defaults partd 0.3.9 py36_0 defaults path.py 11.5.0 py36_0 defaults pathlib2 2.3.2 py36_0 defaults patsy 0.5.1 py36_0 defaults pcre 8.42 h378b8a2_0 defaults pep8 1.7.1 py36_0 defaults pexpect 4.6.0 py36_0 defaults pickleshare 0.7.5 py36_0 defaults pillow 5.3.0 py36hb68e598_0 defaults pip 18.1 py36_0 defaults pkginfo 1.4.2 py36_1 defaults pluggy 0.8.0 py36_0 defaults ply 3.11 py36_0 defaults prometheus_client 0.4.2 py36_0 defaults prompt_toolkit 2.0.7 py36_0 defaults psutil 5.4.8 py36h1de35cc_0 defaults ptyprocess 0.6.0 py36_0 defaults py 1.7.0 py36_0 defaults pyasn1 0.4.4 py36h28b3542_0 defaults pyasn1-modules 0.2.2 py36_0 defaults pycodestyle 2.4.0 py36_0 defaults pycosat 0.6.3 py36h1de35cc_0 defaults pycparser 2.19 py36_0 defaults pycrypto 2.6.1 py36h1de35cc_9 defaults pycurl 7.43.0.2 py36hdbc3d79_0 defaults pyflakes 2.0.0 py36_0 defaults pygments 2.2.0 py36h240cd3f_0 defaults pylint 2.1.1 py36_0 defaults pyodbc 4.0.24 py36h0a44026_0 defaults pyopenssl 18.0.0 py36_0 defaults pyparsing 2.3.0 py36_0 defaults pyqt 5.9.2 py36h655552a_2 defaults pysocks 1.6.8 py36_0 defaults pytables 3.4.4 py36h13cba08_0 defaults pytest 3.10.0 py36_0 defaults pytest-arraydiff 0.2 py36h39e3cac_0 defaults pytest-astropy 0.4.0 py36_0 defaults pytest-cov 2.6.0 py36_0 defaults pytest-doctestplus 0.1.3 py36_0 defaults pytest-openfiles 0.3.0 py36_0 defaults pytest-remotedata 0.3.1 py36_0 defaults python 3.6.6 hc167b69_0 defaults python-dateutil 2.7.5 py36_0 defaults python-libarchive-c 2.8 py36_6 defaults python.app 2 py36_9 defaults pytz 2018.7 py36_0 defaults pywavelets 1.0.1 py36h1d22016_0 defaults pyyaml 3.13 py36h1de35cc_0 defaults pyzmq 17.1.2 py36h1de35cc_0 defaults qt 5.9.6 h45cd832_2 defaults qtawesome 0.5.2 py36_0 defaults qtconsole 4.4.2 py36_0 defaults qtpy 1.5.2 py36_0 defaults readline 7.0 h1de35cc_5 defaults requests 2.20.0 py36_0 defaults rope 0.11.0 py36_0 defaults ruamel_yaml 0.15.46 py36h1de35cc_0 defaults scikit-image 0.14.0 py36h0a44026_1 defaults scikit-learn 0.20.0 py36h4f467ca_1 defaults scipy 1.1.0 py36h28f7352_1 defaults seaborn 0.9.0 py36_0 defaults send2trash 1.5.0 py36_0 defaults service_identity 17.0.0 py36h28b3542_0 defaults setuptools 40.5.0 py36_0 defaults simplegeneric 0.8.1 py36_2 defaults singledispatch 3.4.0.3 py36hf20db9d_0 defaults sip 4.19.8 py36h0a44026_0 defaults six 1.11.0 py36_1 defaults snappy 1.1.7 he62c110_3 defaults snowballstemmer 1.2.1 py36h6c7b616_0 defaults sortedcollections 1.0.1 py36_0 defaults sortedcontainers 2.0.5 py36_0 defaults sphinx 1.8.1 py36_0 defaults sphinxcontrib 1.0 py36_1 defaults sphinxcontrib-websupport 1.1.0 py36_1 defaults spyder 3.3.1 py36_1 defaults spyder-kernels 0.2.6 py36_0 defaults sqlalchemy 1.2.13 py36h1de35cc_0 defaults sqlite 3.24.0 ha441bb4_0 defaults statsmodels 0.9.0 py36h1d22016_0 defaults sympy 1.3 py36_0 defaults tblib 1.3.2 py36hda67792_0 defaults terminado 0.8.1 py36_1 defaults testpath 0.4.2 py36_0 defaults tk 8.6.8 ha441bb4_0 defaults toolz 0.9.0 py36_0 defaults tornado 5.1.1 py36h1de35cc_0 defaults tqdm 4.28.1 py36h28b3542_0 defaults traitlets 4.3.2 py36h65bd3ce_0 defaults twisted 17.5.0 py36_0 defaults typed-ast 1.1.0 py36h1de35cc_0 defaults unicodecsv 0.14.1 py36he531d66_0 defaults unixodbc 2.3.7 h1de35cc_0 defaults urllib3 1.23 py36_0 defaults virtualenv 16.1.0 wcwidth 0.1.7 py36h8c6ec74_0 defaults webencodings 0.5.1 py36_1 defaults werkzeug 0.14.1 py36_0 defaults wheel 0.32.2 py36_0 defaults widgetsnbextension 3.4.2 py36_0 defaults wrapt 1.10.11 py36h1de35cc_2 defaults xlrd 1.1.0 py36_1 defaults xlsxwriter 1.1.2 py36_0 defaults xlwings 0.14.0 py36_0 defaults xlwt 1.2.0 py36h5ad1178_0 defaults xz 5.2.4 h1de35cc_4 defaults yaml 0.1.7 hc338f04_2 defaults zeromq 4.2.5 h0a44026_1 defaults zict 0.1.3 py36_0 defaults zlib 1.2.11 hf3cbc9b_2 defaults zope 1.0 py36_1 defaults zope.interface 4.6.0 py36h1de35cc_0 defaults zstd 1.3.3 h2a6be3a_0 defaults ```

nehaljwani commented 5 years ago

Functions are not exported by default to be made available in subshells. I'd recommend you do:

source ~/anaconda3/etc/profile.d/conda.sh
conda activate my_env

Closing as non-issue. Feel free to re-open if you feel otherwise.

EDIT In the commands above, replace ~/anaconda3/ with the path to your miniconda / anaconda installation. You can find that out by running: conda info | grep -i 'base environment'

mforbes commented 5 years ago

@nehaljwani How would you do this, for example, in a makefile, and is there a simple way to get the path to conda.sh programmatically (say from the name of the environment or an environment.yml file)?

rbutleriii commented 5 years ago

That seems a messy solution to the issue. Now there is a source line in your bash scripts that has to explicitly reference your conda installation path, making them not very portable.

If you use something like source $CONDA_PREFIX/etc/profile.d/conda.sh to get around this, it then makes the script error in everything but the base environment. You could comment in your script that it can only be run from the base, but again: messy.

Is there a conda variable that always returns your base path regardless of your current location?

stuarteberg commented 5 years ago

@rbutleriii

Is there a conda variable that always returns your base path regardless of your current location?

Try this:

CONDA_BASE=$(conda info --base)

stuarteberg commented 5 years ago

@nehaljwani When conda is installed and a user's .bashrc is modified, should the following lines be added to .bashrc? That might save the users some headache. It enables conda to be called from bash scripts without sourcing $(conda info --base)/etc/profile.d/conda.sh.

export -f conda
export -f __conda_activate
export -f __conda_reactivate
export -f __conda_hashr

shenweihai1 commented 5 years ago

Functions are not exported by default to be made available in subshells. I'd recommend you do:
source ~/anaconda3/etc/profile.d/conda.sh
conda activate my_env
Closing as non-issue. Feel free to re-open if you feel otherwise.

that works perfectly~!!!

kagemusha commented 5 years ago

I'm trying that, but get:

➜  /Users/michael  source ~/miniconda3/etc/profile.d/conda.sh
/Users/michael/miniconda3/etc/profile.d/conda.sh:30: parse error near `}'

I'm on Mojave and installed with Miniconda3-latest-MacOSX-x86_64.pkg

jasonsydes commented 5 years ago

This is not a non-issue @nehaljwani. As a user, I would expect that when I run "conda init", that it would prepare my shell for use of "conda activate" everywhere, including within scripts. But it doesn't.

The expected behavior should be exactly what @mjspeck specified, namely that "conda should activate in a bash script the same way it does on the command line".

@rbutleriii is correct that your proposal of adding the line ~/$MY_CONDA_INSTALLATION/etc/profile.d/conda.sh before calling "conda activate" now directly references your personal conda installation. That means that tools that generate "conda activate" calls (e.g. Nextflow) would have to be hand-patched for them to work correctly.

@stuarteberg proposed a perfectly reasonable solution that works (I tested it and yes it works), namely that conda init could add the following to your ~/.bashrc:

export -f conda
export -f __conda_activate
export -f __conda_reactivate
export -f __conda_hashr

I respectfully ask that you re-open this issue and use @stuarteberg's solution (or some other solution) fulfill the expected behavior requested by @mjspeck (i.e. "conda should activate in a bash script the same way it does on the command line"), because that behavior is (I believe) what conda's users are expecting. @stuarteberg's solution would be very easy to implement, and would indeed drastically reduce headaches.

Thank you!!

leclairm commented 5 years ago

@jasonsydes I fully agree.

I also had to add export -f __add_sys_prefix_to_path to my .bashrc in order to get rid of the __add_sys_prefix_to_path: command not found error.

Also note that, until this get fixed, you need to keep these export statements outside of the # >>> conda initialize >>> block so that it doesn't get removed in case you later run conda init bash

stuarteberg commented 5 years ago

+1 for re-opening

scopatz commented 5 years ago

I have noticed that you can do:

eval "$(conda shell.bash hook)"
conda activate <env-name>

msarahan commented 5 years ago

Happy to reopen this, but we have no intention of doing development on this any time soon. The shell scripts are devilishly complicated, and we don't have time to get into them right now. What looks like a "simple change" may break a terrible number of seemingly unrelated stuff.

Community PRs are most welcome.

f1am3d commented 5 years ago

@mjspeck

for Windows:

Install Git Bash
Open Git Bash
type source ~/anaconda3/etc/profile.d/conda.sh
type conda init
Restart your shell
Profit.

Nilanshrajput commented 5 years ago

@mjspeck

for Windows:

Install Git Bash

Open Git Bash

type source ~/anaconda3/etc/profile.d/conda.sh

type conda init

Restart your shell

Profit.

this works

andrew-schweitzer-analog commented 5 years ago

This fixed the issue in my makefile: https://stackoverflow.com/a/55696820/4279266

bryant1410 commented 5 years ago

I think a cleaner way is:

eval "$(conda shell.bash hook)"
conda activate my_env

SmadusankaB commented 5 years ago

On the windows environment use "anaconda prompt" instead of "command prompt".

Go to search. Type "anaconda prompt" and open it. Then type "conda activate

omry commented 5 years ago

Happy to reopen this, but we have no intention of doing development on this any time soon. The shell scripts are devilishly complicated, and we don't have time to get into them right now. What looks like a "simple change" may break a terrible number of seemingly unrelated stuff.

Community PRs are most welcome.

If you don't trust the project testing enough for doing delicate changes, how can you trust community PRs doing delicate changes?

toxyl commented 5 years ago

It almost feels automation-hostile... for now this seems to work:

echo "export -f conda" >> "$HOME/.bashrc" 
echo "export -f __conda_activate" >> "$HOME/.bashrc" 
echo "export -f __conda_reactivate" >> "$HOME/.bashrc" 
echo "export -f __conda_hashr" >> "$HOME/.bashrc" 
echo "export -f __add_sys_prefix_to_path" >> "$HOME/.bashrc" 
echo 'eval "$(conda shell.bash hook)"' >> "$HOME/.bashrc"

I wonder how long before I run into the next issue....

EDIT: Well, in some cases it does, in others it doesn't. In the latter cases it seems to help to explicitly execute eval "$(conda shell.bash hook)" at the beginning of the script, even though it already ran when .bashrc was sourced...

lmeyerov commented 5 years ago

For those wanting to work around the above suggestions, source activate likely has the expected behavior, and hopefully one day conda activate will work as expected too. (We felt uncomfortable adding any of the above suggestions into a maintained codebase.)

abalter commented 5 years ago

Another solution is to call your script with bash -i to invoke your interactive environment.

@scopatz -- I just learned that little trick as well. Do you have any idea what it does?

scopatz commented 5 years ago

@abalter - yeah it basically builds the activation script in $(conda shell.bash hook) and then runs it in the current interpreter session (eval), which allows conda activate <env-name> to work.

technic commented 5 years ago

@abalter The -i option starts bash in interactive mode that means that it loads your ~/.bashrc file, and you probably have conda activation there.

PallawiSinghal commented 4 years ago

Functions are not exported by default to be made available in subshells. I'd recommend you do:
source ~/anaconda3/etc/profile.d/conda.sh
conda activate my_env
Closing as non-issue. Feel free to re-open if you feel otherwise.

Works perfect for me :) Thanks a ton.

cervantes-loves-ai commented 4 years ago

most cleaner option will be

eval "$(conda shell.bash hook)" conda activate my_env

DoaneAS commented 4 years ago

@abalter The -i option starts bash in interactive mode that means that it loads your ~/.bashrc file, and you probably have conda activation there.

This gets to another question and the reason I was looking at this issue. On linux systems, why is ~/.bashrc modified rather than ~/.bash_profile? A non-interactive shell will not normally source ~/.bashrc.

What is the recommended method to activate a conda environment from a non-interactive shell?

bryant1410 commented 4 years ago

This gets to another question and the reason I was looking at this issue. On linux systems, why is ~/.bashrc modified rather than ~/.bash_profile? A non-interactive shell will not normally source ~/.bashrc.

In Ubuntu (and in other distributions that I can't remember), by default ~/.bash_profile sources ~/.profile, which in turns sources ~/.bashrc. So ~/.bashrc will be loaded regardless of it's interactive or not.

hzitoun commented 4 years ago

I have noticed that you can do:
eval "$(conda shell.bash hook)"
conda activate <env-name>

Helped activating my prod env when building my docker image :)

ChrisBarker-NOAA commented 4 years ago

So this is gotten to be a pretty confusing thread.

@msarahan: I understand that this is a complicated process, and conda does not want to add anything to conda without through testing, but for now:

Is there a recommendation for how to automate manipulation of conda environments? My use case at hand is to want to automate start up scripts -- make an environment, add some packages, active it, run an app in it.

It seems there is not recommended way to do that with a shell script.

Would a python script be easier?

Or do we just give up and not try to use conda environments in that way at this point?

Thanks

richerve commented 4 years ago

The eval and then activate option works on direnv too, that basically spawns bash to collect exported variables or execute commands

Natemen96 commented 4 years ago

Adding eval "$(conda shell.bash hook)" to bashrc automatically resolve this issue on startup for Git Bash within Vscode.

cervantes-loves-ai commented 4 years ago

source ~/anaconda3/etc/profile.d/conda.sh conda activate my_env

thank you so much

avoidik commented 4 years ago

it doesn't work on cygwin, it has failed with the error message

$ source /cygdrive/c/tools/miniconda/etc/profile.d/conda.sh
$ conda activate base
$ conda env list
: No such file or directoryiconda/Scripts/conda.exe
$

more verbose log output

Click to expand

``` $ source /cygdrive/c/tools/miniconda/etc/profile.d/conda.sh + source /cygdrive/c/tools/miniconda/etc/profile.d/conda.sh ++ export CONDA_EXE=C:/tools/miniconda/Scripts/conda.exe ++ CONDA_EXE=C:/tools/miniconda/Scripts/conda.exe ++ export _CE_M= ++ _CE_M= ++ export _CE_CONDA= ++ _CE_CONDA= ++ export CONDA_PYTHON_EXE=C:/tools/miniconda/python.exe ++ CONDA_PYTHON_EXE=C:/tools/miniconda/python.exe ++ '[' -z '' ']' ++ export CONDA_SHLVL=0 ++ CONDA_SHLVL=0 ++ '[' -n x ']' ++ '[' -n x ']' +++ dirname C:/tools/miniconda/Scripts/conda.exe ++ PATH=C:/tools/miniconda/Scripts/condabin:/usr/local/bin:/usr/bin ++ export PATH ++ '[' -z x ']' $ conda activate base + conda activate base + '[' 2 -lt 1 ']' + local cmd=activate + shift + case "$cmd" in + __conda_activate activate base + '[' -n '' ']' + local cmd=activate + shift + local ask_conda + CONDA_INTERNAL_OLDPATH=C:/tools/miniconda/Scripts/condabin:/usr/local/bin:/usr/bin + __add_sys_prefix_to_path + '[' -n '' ']' ++ dirname C:/tools/miniconda/Scripts/conda.exe + SYSP=C:/tools/miniconda/Scripts ++ dirname C:/tools/miniconda/Scripts + SYSP=C:/tools/miniconda + '[' -n x ']' + PATH=C:/tools/miniconda/bin:C:/tools/miniconda/Scripts/condabin:/usr/local/bin:/usr/bin + PATH=C:/tools/miniconda/Scripts:C:/tools/miniconda/bin:C:/tools/miniconda/Scripts/condabin:/usr/local/bin:/usr/bin + PATH=C:/tools/miniconda/Library/bin:C:/tools/miniconda/Scripts:C:/tools/miniconda/bin:C:/tools/miniconda/Scripts/condabin:/usr/local/bin:/usr/bin + PATH=C:/tools/miniconda/Library/usr/bin:C:/tools/miniconda/Library/bin:C:/tools/miniconda/Scripts:C:/tools/miniconda/bin:C:/tools/miniconda/Scripts/condabin:/usr/local/bin:/usr/bin + PATH=C:/tools/miniconda/Library/mingw-w64/bin:C:/tools/miniconda/Library/usr/bin:C:/tools/miniconda/Library/bin:C:/tools/miniconda/Scripts:C:/tools/miniconda/bin:C:/tools/miniconda/Scripts/condabin:/usr/local/bin:/usr/bin + PATH=C:/tools/miniconda:C:/tools/miniconda/Library/mingw-w64/bin:C:/tools/miniconda/Library/usr/bin:C:/tools/miniconda/Library/bin:C:/tools/miniconda/Scripts:C:/tools/miniconda/bin:C:/tools/miniconda/Scripts/condabin:/usr/local/bin:/usr/bin + export PATH ++ PS1='\[\e]0;\w\a\]\n\[\e[32m\]\u@\h \[\e[33m\]\w\[\e[0m\]\n\$ ' ++ C:/tools/miniconda/Scripts/conda.exe shell.posix activate base + ask_conda='PS1='\''(base) \[\e]0;\w\a\]\n\[\e[32m\]\u@\h \[\e[33m\]\w\[\e[0m\]\n\$ '\'' export PATH='\''/cygdrive/c/tools/miniconda:/cygdrive/c/tools/miniconda/Library/mingw-w64/bin:/cygdrive/c/tools/miniconda/Library/usr/bin:/cygdrive/c/tools/miniconda/Library/bin:/cygdrive/c/tools/miniconda/Scripts:/cygdrive/c/tools/miniconda/bin:C:/tools/miniconda:C:/tools/miniconda/Library/mingw-w64/bin:C:/tools/miniconda/Library/usr/bin:C:/tools/miniconda/Library/bin:C:/tools/miniconda/Scripts:C:/tools/miniconda/bin:C:/tools/miniconda/Scripts/condabin:/usr/local/bin:/usr/bin'\'' export CONDA_PREFIX='\''C:\tools\miniconda'\'' export CONDA_SHLVL='\''1'\'' export CONDA_DEFAULT_ENV='\''base'\'' export CONDA_PROMPT_MODIFIER='\''(base) '\'' export CONDA_EXE='\''/cygdrive/c/tools/miniconda/Scripts/conda.exe'\'' export _CE_M='\'''\'' export _CE_CONDA='\'''\'' 'xport CONDA_PYTHON_EXE='\''/cygdrive/c/tools/miniconda/python.exe'\'' + rc=0 + PATH=C:/tools/miniconda/Scripts/condabin:/usr/local/bin:/usr/bin + eval 'PS1='\''(base) \[\e]0;\w\a\]\n\[\e[32m\]\u@\h \[\e[33m\]\w\[\e[0m\]\n\$ '\'' export PATH='\''/cygdrive/c/tools/miniconda:/cygdrive/c/tools/miniconda/Library/mingw-w64/bin:/cygdrive/c/tools/miniconda/Library/usr/bin:/cygdrive/c/tools/miniconda/Library/bin:/cygdrive/c/tools/miniconda/Scripts:/cygdrive/c/tools/miniconda/bin:C:/tools/miniconda:C:/tools/miniconda/Library/mingw-w64/bin:C:/tools/miniconda/Library/usr/bin:C:/tools/miniconda/Library/bin:C:/tools/miniconda/Scripts:C:/tools/miniconda/bin:C:/tools/miniconda/Scripts/condabin:/usr/local/bin:/usr/bin'\'' export CONDA_PREFIX='\''C:\tools\miniconda'\'' export CONDA_SHLVL='\''1'\'' export CONDA_DEFAULT_ENV='\''base'\'' export CONDA_PROMPT_MODIFIER='\''(base) '\'' export CONDA_EXE='\''/cygdrive/c/tools/miniconda/Scripts/conda.exe'\'' export _CE_M='\'''\'' export _CE_CONDA='\'''\'' 'xport CONDA_PYTHON_EXE='\''/cygdrive/c/tools/miniconda/python.exe'\'' '+ PS1='(base) \[\e]0;\w\a\]\n\[\e[32m\]\u@\h \[\e[33m\]\w\[\e[0m\]\n\$ ++ export $'PATH=/cygdrive/c/tools/miniconda:/cygdrive/c/tools/miniconda/Library/mingw-w64/bin:/cygdrive/c/tools/miniconda/Library/usr/bin:/cygdrive/c/tools/miniconda/Library/bin:/cygdrive/c/tools/miniconda/Scripts:/cygdrive/c/tools/miniconda/bin:C:/tools/miniconda:C:/tools/miniconda/Library/mingw-w64/bin:C:/tools/miniconda/Library/usr/bin:C:/tools/miniconda/Library/bin:C:/tools/miniconda/Scripts:C:/tools/miniconda/bin:C:/tools/miniconda/Scripts/condabin:/usr/local/bin:/usr/bin\r' ++ PATH=$'/cygdrive/c/tools/miniconda:/cygdrive/c/tools/miniconda/Library/mingw-w64/bin:/cygdrive/c/tools/miniconda/Library/usr/bin:/cygdrive/c/tools/miniconda/Library/bin:/cygdrive/c/tools/miniconda/Scripts:/cygdrive/c/tools/miniconda/bin:C:/tools/miniconda:C:/tools/miniconda/Library/mingw-w64/bin:C:/tools/miniconda/Library/usr/bin:C:/tools/miniconda/Library/bin:C:/tools/miniconda/Scripts:C:/tools/miniconda/bin:C:/tools/miniconda/Scripts/condabin:/usr/local/bin:/usr/bin\r' '+ export 'CONDA_PREFIX=C:\tools\miniconda '+ CONDA_PREFIX='C:\tools\miniconda ++ export $'CONDA_SHLVL=1\r' ++ CONDA_SHLVL=$'1\r' ++ export $'CONDA_DEFAULT_ENV=base\r' ++ CONDA_DEFAULT_ENV=$'base\r' '+ export 'CONDA_PROMPT_MODIFIER=(base) '+ CONDA_PROMPT_MODIFIER='(base) ++ export $'CONDA_EXE=/cygdrive/c/tools/miniconda/Scripts/conda.exe\r' ++ CONDA_EXE=$'/cygdrive/c/tools/miniconda/Scripts/conda.exe\r' ++ export $'_CE_M=\r' ++ _CE_M=$'\r' ++ export $'_CE_CONDA=\r' ++ _CE_CONDA=$'\r' ++ export $'CONDA_PYTHON_EXE=/cygdrive/c/tools/miniconda/python.exe\r' ++ CONDA_PYTHON_EXE=$'/cygdrive/c/tools/miniconda/python.exe\r' + '[' 0 '!=' 0 ']' + __conda_hashr + '[' -n '' ']' + '[' -n '' ']' + hash -r (base) conda env list + conda env list + '[' 2 -lt 1 ']' + local cmd=env + shift + case "$cmd" in + CONDA_INTERNAL_OLDPATH=$'/cygdrive/c/tools/miniconda:/cygdrive/c/tools/miniconda/Library/mingw-w64/bin:/cygdrive/c/tools/miniconda/Library/usr/bin:/cygdrive/c/tools/miniconda/Library/bin:/cygdrive/c/tools/miniconda/Scripts:/cygdrive/c/tools/miniconda/bin:C:/tools/miniconda:C:/tools/miniconda/Library/mingw-w64/bin:C:/tools/miniconda/Library/usr/bin:C:/tools/miniconda/Library/bin:C:/tools/miniconda/Scripts:C:/tools/miniconda/bin:C:/tools/miniconda/Scripts/condabin:/usr/local/bin:/usr/bin\r' + __add_sys_prefix_to_path + '[' -n $'\r' ']' + '[' -n x ']' ++ dirname $'/cygdrive/c/tools/miniconda/Scripts/conda.exe\r' bash: dirname: command not found + SYSP= + '[' -n x ']' + PATH=$'/bin:/cygdrive/c/tools/miniconda:/cygdrive/c/tools/miniconda/Library/mingw-w64/bin:/cygdrive/c/tools/miniconda/Library/usr/bin:/cygdrive/c/tools/miniconda/Library/bin:/cygdrive/c/tools/miniconda/Scripts:/cygdrive/c/tools/miniconda/bin:C:/tools/miniconda:C:/tools/miniconda/Library/mingw-w64/bin:C:/tools/miniconda/Library/usr/bin:C:/tools/miniconda/Library/bin:C:/tools/miniconda/Scripts:C:/tools/miniconda/bin:C:/tools/miniconda/Scripts/condabin:/usr/local/bin:/usr/bin\r' + PATH=$'/Scripts:/bin:/cygdrive/c/tools/miniconda:/cygdrive/c/tools/miniconda/Library/mingw-w64/bin:/cygdrive/c/tools/miniconda/Library/usr/bin:/cygdrive/c/tools/miniconda/Library/bin:/cygdrive/c/tools/miniconda/Scripts:/cygdrive/c/tools/miniconda/bin:C:/tools/miniconda:C:/tools/miniconda/Library/mingw-w64/bin:C:/tools/miniconda/Library/usr/bin:C:/tools/miniconda/Library/bin:C:/tools/miniconda/Scripts:C:/tools/miniconda/bin:C:/tools/miniconda/Scripts/condabin:/usr/local/bin:/usr/bin\r' + PATH=$'/Library/bin:/Scripts:/bin:/cygdrive/c/tools/miniconda:/cygdrive/c/tools/miniconda/Library/mingw-w64/bin:/cygdrive/c/tools/miniconda/Library/usr/bin:/cygdrive/c/tools/miniconda/Library/bin:/cygdrive/c/tools/miniconda/Scripts:/cygdrive/c/tools/miniconda/bin:C:/tools/miniconda:C:/tools/miniconda/Library/mingw-w64/bin:C:/tools/miniconda/Library/usr/bin:C:/tools/miniconda/Library/bin:C:/tools/miniconda/Scripts:C:/tools/miniconda/bin:C:/tools/miniconda/Scripts/condabin:/usr/local/bin:/usr/bin\r' + PATH=$'/Library/usr/bin:/Library/bin:/Scripts:/bin:/cygdrive/c/tools/miniconda:/cygdrive/c/tools/miniconda/Library/mingw-w64/bin:/cygdrive/c/tools/miniconda/Library/usr/bin:/cygdrive/c/tools/miniconda/Library/bin:/cygdrive/c/tools/miniconda/Scripts:/cygdrive/c/tools/miniconda/bin:C:/tools/miniconda:C:/tools/miniconda/Library/mingw-w64/bin:C:/tools/miniconda/Library/usr/bin:C:/tools/miniconda/Library/bin:C:/tools/miniconda/Scripts:C:/tools/miniconda/bin:C:/tools/miniconda/Scripts/condabin:/usr/local/bin:/usr/bin\r' + PATH=$'/Library/mingw-w64/bin:/Library/usr/bin:/Library/bin:/Scripts:/bin:/cygdrive/c/tools/miniconda:/cygdrive/c/tools/miniconda/Library/mingw-w64/bin:/cygdrive/c/tools/miniconda/Library/usr/bin:/cygdrive/c/tools/miniconda/Library/bin:/cygdrive/c/tools/miniconda/Scripts:/cygdrive/c/tools/miniconda/bin:C:/tools/miniconda:C:/tools/miniconda/Library/mingw-w64/bin:C:/tools/miniconda/Library/usr/bin:C:/tools/miniconda/Library/bin:C:/tools/miniconda/Scripts:C:/tools/miniconda/bin:C:/tools/miniconda/Scripts/condabin:/usr/local/bin:/usr/bin\r' + PATH=$':/Library/mingw-w64/bin:/Library/usr/bin:/Library/bin:/Scripts:/bin:/cygdrive/c/tools/miniconda:/cygdrive/c/tools/miniconda/Library/mingw-w64/bin:/cygdrive/c/tools/miniconda/Library/usr/bin:/cygdrive/c/tools/miniconda/Library/bin:/cygdrive/c/tools/miniconda/Scripts:/cygdrive/c/tools/miniconda/bin:C:/tools/miniconda:C:/tools/miniconda/Library/mingw-w64/bin:C:/tools/miniconda/Library/usr/bin:C:/tools/miniconda/Library/bin:C:/tools/miniconda/Scripts:C:/tools/miniconda/bin:C:/tools/miniconda/Scripts/condabin:/usr/local/bin:/usr/bin\r' + export PATH + $'/cygdrive/c/tools/miniconda/Scripts/conda.exe\r' $'\r' $'\r' env list : No such file or directoryiconda/Scripts/conda.exe + local t1=127 + PATH=$'/cygdrive/c/tools/miniconda:/cygdrive/c/tools/miniconda/Library/mingw-w64/bin:/cygdrive/c/tools/miniconda/Library/usr/bin:/cygdrive/c/tools/miniconda/Library/bin:/cygdrive/c/tools/miniconda/Scripts:/cygdrive/c/tools/miniconda/bin:C:/tools/miniconda:C:/tools/miniconda/Library/mingw-w64/bin:C:/tools/miniconda/Library/usr/bin:C:/tools/miniconda/Library/bin:C:/tools/miniconda/Scripts:C:/tools/miniconda/bin:C:/tools/miniconda/Scripts/condabin:/usr/local/bin:/usr/bin\r' + return 127 (base) ```

for some reason conda init bash doesn't respect line-feeds, converting them to CRLF, then in conda.sh we see CRs or '\r', also CONDA_PREFIX returned as Windows-native path

$ /cygdrive/c/tools/miniconda/Scripts/conda.exe shell.posix activate base
+ /cygdrive/c/tools/miniconda/Scripts/conda.exe shell.posix activate base
PS1='(base) \[\033[1;36m\]18:50:35\[\e[0m\] \[\033[1;34m\]\w\[\e[0m\] \[\033[1;31m\]$\[\e[0m\] '
export PATH='/cygdrive/c/tools/miniconda:/cygdrive/c/tools/miniconda/Library/mingw-w64/bin:/cygdrive/c/tools/miniconda/Library/usr/bin:/cygdrive/c/too
ls/miniconda/Library/bin:/cygdrive/c/tools/miniconda/Scripts:/cygdrive/c/tools/miniconda/bin:/cygdrive/c/tools/miniconda/condabin:/usr/local/bin:/usr/
bin'
export CONDA_PREFIX='C:\tools\miniconda'
export CONDA_SHLVL='1'
export CONDA_DEFAULT_ENV='base'
export CONDA_PROMPT_MODIFIER='(base) '
export CONDA_EXE='/cygdrive/c/tools/miniconda/Scripts/conda.exe'
export _CE_M=''
export _CE_CONDA=''
export CONDA_PYTHON_EXE='/cygdrive/c/tools/miniconda/python.exe'

mingwandroid commented 4 years ago

We do not support Cygwin yet. PRs welcome. The only Unix shells we support at present are the MSYS2 shell and Git for Windows.

kathoef commented 4 years ago

I have stumpled across this problem a few days ago, too. Apparently, conda is not fully/properly initialised for non-interactive shell sessions/environments.

I am using bash, and have set up a JupyterLab with conda in my home directory doing

wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh -b -p miniconda3
${HOME}/miniconda3/bin/conda init bash
${HOME}/miniconda3/bin/conda config --set auto_activate_base false
${HOME}/miniconda3/bin/conda install -n base jupyterlab

If I do in a fresh bash login session (on an HPC system, but that is not really important here)

conda activate base && jupyter lab --ip=$(hostname) --no-browser

then everything works as expected. If I set up a bash script that contains

#!/bin/bash
conda activate base && jupyter lab --ip=$(hostname) --no-browser

and that I execute with

./jupyterlab.sh

I get the following error

CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'.
To initialize your shell, run

    $ conda init <SHELL_NAME>

[...]

As my .bashrc already contains the necessary conda initialisation part, I tried to investigate the problem a little bit deeper, and have found my script to work if I explicitely set an interactive bash environment by using the interactive flag in the header

#!/bin/bash -i
conda activate base && jupyter lab --ip=$(hostname) --no-browser

In the end, however, I have decided to go with

#!/usr/bin/env bash
eval "$(conda shell.bash hook)" # properly initialise non-interactive shell
conda activate base && \
jupyter lab --ip=$(hostname) --no-browser

which also works as expected.

I don't really know, if this is of any help here. But I wanted to leave a quick note about the aspect of interactive vs. non-interactive shell sessions/environments, that has not yet explicitely been mentioned above.

(For completion, I have Ubuntu 18.04.4 LTS with bash 4.4.20 and conda 4.8.3.)

brisk022 commented 4 years ago

@kathoef Somebody decided in the name of efficiency (?) to place the following code in the default .bashrc

# If not running interactively, don't do anything
case $- in
    *i*) ;;
      *) return;;
esac

Conda initialisation code is inserted at the end of .bashrc. So, the sourcing terminates before the conda initialisation code is reached.

The issue had been bugging me for over a year until I decided to review .bashrc line by line from the beginning and discovered the culprit.

For portability, I currently use the following code:

if [[ -n "$CONDA_EXE" ]]; then
   condaSetup="$($CONDA_EXE 'shell.bash' 'hook' 2> /dev/null)"
   eval "$condaSetup"
else
   if [[ -n "$CONDA_PREFIX" ]]; then
      source ${CONDA_PREFIX%/envs/*}/etc/profile.d/conda.sh
   else
      echo "Unable to initialise conda function. Please check if CONDA variables are exported."
   fi
fi

That works fine as long as you init conda in .bashrc and your job scheduling system passes the environmental variables on.

avoidik commented 4 years ago

if you'd run a terminal interactively it should work just fine, for example in ubuntu and friends this option usually disabled by default

avoidik commented 4 years ago

you may solve cygwin issue on Windows by creating a new global environment variable SHELLOPTS=igncr and setting relevant paths manually

JivanRoquet commented 4 years ago

source ~/anaconda3/etc/profile.d/conda.sh conda activate

@nehaljwani, thanks, much, works perfectly

@lboy27282 you should add "works perfectly on your machine". And this is why nehaljwani's answer was downvoted so much.

Try porting your script to a prod environment where conda installation path might be different and you'll see what I mean.

cs145442 commented 4 years ago

I've created a conda environment as well as added the path in Google Colab

import sys _ = (sys.path .append("/usr/local/lib/python3.6/site-packages"))

But while activating the environment, It throws the following error.

Screenshot 2020-07-15 at 3 10 09 PM

Also tried as suggested earlier, but I'm not sure where the profile.d/conda.sh is located in my colab notebook.

Screenshot 2020-07-15 at 3 10 34 PM

I'm not sure what is it related to. I know its tricky to work with Google Colab but I'm hoping to get some help here. Thanks.

Also, the environment is successfully listed in the condo env list as below.

Screenshot 2020-07-15 at 3 07 22 PM

Thanks for finding some time for this. I hope it's resolvable in due time.

ChrisBarker-NOAA commented 4 years ago

I know nothing of Google Colab, but:

sys.path .append("/usr/local/lib/python3.6/site-packages")

Is a Bad Idea -- you really don't want to mix system with conda environments. It's kind of the point to NOT use usr/local -- that's why you have conda.

leofang commented 4 years ago

you should add "works perfectly on your machine". And this is why nehaljwani's answer was downvoted so much.

@JivanRoquet You're not being fair. Why don't you say @nehaljwani's answer was upvoted so much? Before this issue is officially fixed (which is surprising that we're already in 2020 and it still is not!), it is the easiest solution to try first.

iterateself commented 4 years ago

@mjspeck

for Windows:

Install Git Bash

Open Git Bash

type source ~/anaconda3/etc/profile.d/conda.sh

type conda init

Restart your shell

Profit.

and in sh:

I think a cleaner way is:
eval "$(conda shell.bash hook)"
conda activate my_env

this works

osharaki commented 4 years ago

@mjspeck

for Windows:

Install Git Bash

Open Git Bash

type source ~/anaconda3/etc/profile.d/conda.sh

type conda init

Restart your shell

Profit.

Any idea how to undo this? Now whenever I open Git bash, it automatically activates the base Conda environment.

avoidik commented 4 years ago

open bash profile file and remove lines added by conda, restart terminal windows

osharaki commented 4 years ago

open bash profile file and remove lines added by conda, restart terminal windows

Thank you, this works. Is there a way to achieve the same effect without having Conda activate automatically every time?

As a side note, it seems conda init disabled the password prompt (SSH agent) that I usually get when opening a new git bash terminal. Can't seem to get it back.

avoidik commented 4 years ago

you may try to disable base env activation by setting configuration parameter:

conda config --set auto_activate_base false

or add this line before init script

export CONDA_AUTO_ACTIVATE_BASE="false"

osharaki commented 4 years ago

you may try to disable base env activation by setting configuration parameter: conda config --set auto_activate_base false or add this line before init script export CONDA_AUTO_ACTIVATE_BASE="false"

Where can I find the init script?

avoidik commented 4 years ago

the lines added by conda to your bash profile file is init script

osharaki commented 4 years ago

@mjspeck

for Windows:

Install Git Bash

Open Git Bash

type source ~/anaconda3/etc/profile.d/conda.sh

type conda init

Restart your shell

Profit.

For anyone else trying this, this only worked for me when I typed conda init bash in step 4. However, if you're using an SSH agent, this will prevent the password prompt from appearing.

conda / conda